X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=f268d377ff1a7d6f78d702cae7e65b144c8fd9af;hb=8ec36c3e36ff5beb0db07345babe8c8426d0426b;hp=5733719a9607fec5928912e5296a37253b1851ec;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 5733719..f268d37 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -28,6 +28,7 @@ import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
@@ -1471,8 +1472,8 @@ public class Alignment implements AlignmentI
   {
     // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
-    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
+    boolean samegap = oldc == getGapCharacter();
     boolean hashidden = toappend.getHiddenSequences() != null
             && toappend.getHiddenSequences().hiddenSequences != null;
     // get all sequences including any hidden ones
@@ -1490,14 +1491,7 @@ public class Alignment implements AlignmentI
         {
           if (!samegap)
           {
-            char[] oldseq = addedsq.getSequence();
-            for (int c = 0; c < oldseq.length; c++)
-            {
-              if (oldseq[c] == oldc)
-              {
-                oldseq[c] = gapCharacter;
-              }
-            }
+            addedsq.replace(oldc, gapCharacter);
           }
           toappendsq.add(addedsq);
         }
@@ -1624,40 +1618,21 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<>();
     AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
     if (alignmentAnnotation != null)
     {
-      for (AlignmentAnnotation a : alignmentAnnotation)
-      {
-        if (a.getCalcId() == calcId || (a.getCalcId() != null
-                && calcId != null && a.getCalcId().equals(calcId)))
-        {
-          aa.add(a);
-        }
-      }
+      return AlignmentAnnotation.findAnnotation(
+              Arrays.asList(getAlignmentAnnotation()), calcId);
     }
-    return aa;
+    return Arrays.asList(new AlignmentAnnotation[] {});
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if ((calcId == null || (ann.getCalcId() != null
-              && ann.getCalcId().equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null
-                      && ann.sequenceRef == seq))
-              && (label == null
-                      || (ann.label != null && ann.label.equals(label))))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   @Override